Ok so I have been lurking for days to find a way to analyse my data, often ending up here... but I haven't found a satisfying answer yet. Lots of answers poping-up are 5+ years old. I am still part of the newbie gang. So here I come with a bunch of questions.
I have a few sets of ±100 proteins identified by MS as up/down-regulated under a few conditions. So I am looking for an easy workflow to obtain a scientifically accurate network, stringent enough to stay away from false positives although not TOO stringent so I can actually get some informations from my diverse network. As well as a pretty figure at the end to show off with :) I have Uniprot IDs, a fold change and a p-value. Rather looking for free apps (OS X) or web-based tools.
My idea is to end up on cytoscape to finalise some neat protein networks.
Based on direct physical interactions > common pathway/function > genetic interactions (it seems to dilute the essential information?). Rather experimental than predicted.
With a color code for up/down-regulated, scaled according to my fold change.
Maybe a shape code for molecular function/protein class.
A node size scaled to the number of edges (already mastering that one)
With also a clear identification of functional groups (biological process/pathway).
And several type of connections according to the source.
To give you an example of what I have in mind: http://www.nature.com/nbt/journal/v30/n10/full/nbt.2356.html (They use MetaCore which I don't have access to...)
First of all, Uniprot IDs... Somehow there's always some proteins that are left behind as the IDs are not being accurately recognised. I have checked and corrected them if necessary, my (human) IDs are up to date on Uniprot.org. How come? Do I have to just live with that?
Ingenuity, iPathway, Reactome don't seem to answer my needs.
Best tool to build my network:
STRING, I was quite happy with it at first but it smells like a trap. How to avoid false positives? Sources? Minimum score (0,7?), Max number of interactors to show (1st, 2d shell?)
GeneMANIA is quite seducing, all pretty and simple. I can actually select the kind of sources I am looking for... but way more hits than STRING. Lacking a score threshold? No control over it..
ConsensusPathDB. For what I've read, it seems to be THE ONE but it crashes with over 9000 listed interactions on my computer and for what I've seen it's pretty basic?
Cytoscape in-Apps: String, Genemania, Reactome... none seems to work as good as the web-based tools.
How do I impute any external data (Fold change, GO stuff, ...) to my network coming from STRING or GeneMANIA let say? I have a file for the network and a file with FC values etc...
I've read about GOlorize, BiNGO, iRegulon, ClusterViz, EnrichmentMap... where to go?
I don't feel like I am asking the moon. But we're in 2017 and I can't be the first one with that kind of request. How come it is so difficult? diluted within so many options? and there's no easy way to go? I don't mind "getting my hands dirty" but it seems endless here...
So, any solid workflow to follow?